A DNA Virus of Drosophila

Little is known about the viruses infecting most species. Even in groups as well-studied as Drosophila, only a handful of viruses have been well-characterized. A viral metagenomic approach was used to explore viral diversity in 83 wild-caught Drosophila innubila, a mushroom feeding member of the quinaria group. A single fly that was injected with, and died from, Drosophila C Virus (DCV) was added to the sample as a control. Two-thirds of reads in the infected sample had DCV as the best BLAST hit, suggesting that the protocol developed is highly sensitive. In addition to the DCV hits, several sequences had Oryctes rhinoceros Nudivirus, a double-stranded DNA virus, as a best BLAST hit. The virus associated with these sequences was termed Drosophila innubila Nudivirus (DiNV). PCR screens of natural populations showed that DiNV was both common and widespread taxonomically and geographically. Electron microscopy confirms the presence of virions in fly fecal material similar in structure to other described Nudiviruses. In 2 species, D. innubila and D. falleni, the virus is associated with a severe (∼80–90%) loss of fecundity and significantly decreased lifespan

Potential Costs of Acclimatization to a Warmer Climate: Growth of a Reef Coral with Heat Tolerant vs. Sensitive Symbiont Types

One of the principle ways in which reef building corals are likely to cope with a warmer climate is by changing to more thermally tolerant endosymbiotic algae (zooxanthellae) genotypes. It is highly likely that hosting a more heat-tolerant algal genotype will be accompanied by tradeoffs in the physiology of the coral. To better understand one of these tradeoffs, growth was investigated in the Indo-Pacific reef-building coral Acropora millepora in both the laboratory and the field. In the Keppel Islands in the southern Great Barrier Reef this species naturally harbors nrDNA ITS1 thermally sensitive type C2 or thermally tolerant type D zooxanthellae of the genus Symbiodinium and can change dominant type following bleaching. We show that under controlled conditions, corals with type D symbionts grow 29% slower than those with type C2 symbionts. In the field, type D colonies grew 38% slower than C2 colonies. These results demonstrate the magnitude of trade-offs likely to be experienced by this species as they acclimatize to warmer conditions by changing to more thermally tolerant type D zooxanthellae. Irrespective of symbiont genotype, corals were affected to an even greater degree by the stress of a bleaching event which reduced growth by more than 50% for up to 18 months compared to pre-bleaching rates. The processes of symbiont change and acute thermal stress are likely to act in concert on coral growth as reefs acclimatize to more stressful warmer conditions, further compromising their regeneration capacity following climate change

Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level

We tested the metabolic rate hypothesis (whereby rates of mtDNA evolution are postulated to be mediated primarily by mutagenic by-products of respiration) by examining whether mass-specific metabolic rate was correlated with root-to-tip distance on a set of mtDNA trees for the springtail Cryptopygus antarcticus travei from sub-Antarctic Marion Island

Concomitant Duplications of Opioid Peptide and Receptor Genes before the Origin of Jawed Vertebrates

Background: The opioid system is involved in reward and pain mechanisms and consists in mammals of four receptors an

Genetic Diversity and Connectivity in the Threatened Staghorn Coral (Acropora cervicornis) in Florida

Over the past three decades, populations of the dominant shallow water Caribbean corals, Acropora cervicornis and A. palmata, have been devastated by white-band disease (WBD), resulting in the listing of both species as threatened under the U.S. Endangered Species Act. A key to conserving these threatened corals is understanding how their populations are genetically interconnected throughout the greater Caribbean. Genetic research has demonstrated that gene flow is regionally restricted across the Caribbean in both species. Yet, despite being an important site of coral reef research, little genetic data has been available for the Florida Acropora, especially for the staghorn coral, A. cervicornis. In this study, we present new mitochondrial DNA sequence data from 52 A. cervicornis individuals from 22 sites spread across the upper and lower Florida Keys, which suggest that Florida's A. cervicornis populations are highly genetically interconnected (FST = −0.081). Comparison between Florida and existing mtDNA data from six regional Caribbean populations indicates that Florida possesses high levels of standing genetic diversity (h = 0.824) relative to the rest of the greater Caribbean (h = 0.701±0.043). We find that the contemporary level of gene flow across the greater Caribbean, including Florida, is restricted ( = 0.117), but evidence from shared haplotypes suggests the Western Caribbean has historically been a source of genetic variation for Florida. Despite the current patchiness of A. cervicornis in Florida, the relatively high genetic diversity and connectivity within Florida suggest that this population may have sufficient genetic variation to be viable and resilient to environmental perturbation and disease. Limited genetic exchange across regional populations of the greater Caribbean, including Florida, indicates that conservation efforts for A. cervicornis should focus on maintaining and managing populations locally rather than relying on larval inputs from elsewhere

The Sixth Rhino: A Taxonomic Re-Assessment of the Critically Endangered Northern White Rhinoceros

BACKGROUND: The two forms of white rhinoceros; northern and southern, have had contrasting conservation histories. The Northern form, once fairly numerous is now critically endangered, while the southern form has recovered from a few individuals to a population of a few thousand. Since their last taxonomic assessment over three decades ago, new material and analytical techniques have become available, necessitating a review of available information and re-assessment of the taxonomy. RESULTS: Dental morphology and cranial anatomy clearly diagnosed the southern and northern forms. The differentiation was well supported by dental metrics, cranial growth and craniometry, and corresponded with differences in post-cranial skeleton, external measurements and external features. No distinctive differences were found in the limited descriptions of their behavior and ecology. Fossil history indicated the antiquity of the genus, dating back at least to early Pliocene and evolution into a number of diagnosable forms. The fossil skulls examined fell outside the two extant forms in the craniometric analysis. Genetic divergence between the two forms was consistent across both nuclear and mitochondrial genomes, and indicated a separation of over a million years. CONCLUSIONS: On re-assessing the taxonomy of the two forms we find them to be morphologically and genetically distinct, warranting the recognition of the taxa formerly designated as subspecies; Ceratotherium simum simum the southern form and Ceratotherium simum cottoni the northern form, as two distinct species Ceratotherium simum and Ceratotherium cottoni respectively. The recognition of the northern form as a distinct species has profound implications for its conservation

Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling

Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5–25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes

Multiple Origins of Elytral Reticulation Modifications in the West Palearctic Agabus bipustulatus Complex (Coleoptera, Dytiscidae)

The Agabus bipustulatus complex includes one of Europe's most widely distributed and common diving beetles. This complex, which is known for its large morphological variation, has a complex demographic and altitudinal variation in elytral reticulation. The various depth of the reticulation imprint, both in smaller and larger meshes, results in both mat and shiny individuals, as well as intermediate forms. The West Palearctic lowland is inhabited by a sexually dimorphic form, with shiny males and mat females. In mountain regions, shiny individuals of both sexes are found intermixed with mat individuals or in pure populations in central and southern areas, whereas pure populations of mat individuals are exclusively found in the northern region at high altitude. Sexual selection is proposed as a driving force in shaping this variation. However, the occurrence of different types of reticulation in both sexes and disjunct geographical distribution patterns suggest an additional function of the reticulation. Here we investigate the phylogeographical history, genetic structure and reticulation variation of several named forms within the Agabus bipustulatus complex including A. nevadensis. The molecular analyses recognised several well-supported clades within the complex. Several of the named forms had two or more independent origins. Few south European populations were uniform in reticulation patterns, and the males were found to display large variation. Reticulation diversity and population genetic variability were clearly correlated to altitude, but no genetic differences were detected among populations with mixed or homogenous forms. Observed reduction in secondary reticulation in female and increased variance in male at high altitude in South Europe may be explained by the occurrence of an additional selective force, beside sexual selection. The combined effect of these selective processes is here demonstrated in an extreme case to generate isolation barriers between populations at high altitudes. Here we discuss this selective force in relation to thermal selection

Reduced Polymorphism Associated with X Chromosome Meiotic Drive in the Stalk-Eyed Fly Teleopsis dalmanni

Sex chromosome meiotic drive has been suggested as a cause of several evolutionary genetic phenomena, including genomic conflicts that give rise to reproductive isolation between new species. In this paper we present a population genetic analysis of X chromosome drive in the stalk-eyed fly, Teleopsis dalmanni, to determine how this natural polymorphism influences genetic diversity. We analyzed patterns of DNA sequence variation at two X-linked regions (comprising 1325 bp) approximately 50 cM apart and one autosomal region (comprising 921 bp) for 50 males, half of which were collected in the field from one of two allopatric locations and the other half were derived from lab-reared individuals with known brood sex ratios. These two populations are recently diverged but exhibit partial postzygotic reproductive isolation, i.e. crosses produce sterile hybrid males and fertile females. We find no nucleotide or microsatellite variation on the drive X chromosome, whereas the same individuals show levels of variation at autosomal regions that are similar to field-collected flies. Furthermore, one field-caught individual collected 10 years previously had a nearly identical X haplotype to the drive X, and is over 2% divergent from other haplotypes sampled from the field. These results are consistent with a selective sweep that has removed genetic variation from much of the drive X chromosome. We discuss how this finding may relate to the rapid evolution of postzygotic reproductive isolation that has been documented for these flies

Anchor-Based Whole Genome Phylogeny (ABWGP): A Tool for Inferring Evolutionary Relationship among Closely Related Microorganims

Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species